HEADER HYDROLASE 22-MAR-23 8OI7 TITLE TRICHOMONAS VAGINALIS RIBOSIDE HYDROLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE FAMILY COMPND 3 PROTEIN; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRICHOMONAS VAGINALIS; SOURCE 3 ORGANISM_TAXID: 5722; SOURCE 4 GENE: TVAG_092730; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NH-FOLD, NUCLEOSIDE HYDROLASE, RIBOSIDE HYDROLASE, NICOTINAMIDE KEYWDS 2 RIBOSIDE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PATRONE,B.J.STOCKMAN,M.DEGANO REVDAT 2 06-SEP-23 8OI7 1 JRNL REVDAT 1 02-AUG-23 8OI7 0 JRNL AUTH M.PATRONE,G.S.GALASYN,F.KERIN,M.M.NYITRAY,D.W.PARKIN, JRNL AUTH 2 B.J.STOCKMAN,M.DEGANO JRNL TITL A RIBOSIDE HYDROLASE THAT SALVAGES BOTH NUCLEOBASES AND JRNL TITL 2 NICOTINAMIDE IN THE AUXOTROPHIC PARASITE TRICHOMONAS JRNL TITL 3 VAGINALIS. JRNL REF J.BIOL.CHEM. V. 299 05077 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37482279 JRNL DOI 10.1016/J.JBC.2023.105077 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0405 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 68100 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.073 REMARK 3 FREE R VALUE TEST SET COUNT : 3455 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4173 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 210 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5467 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.47000 REMARK 3 B22 (A**2) : -1.47000 REMARK 3 B33 (A**2) : 2.93900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.940 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5660 ; 0.004 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5331 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7656 ; 1.038 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12345 ; 0.358 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 694 ; 6.460 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 24 ; 4.990 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 967 ;13.557 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 856 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6432 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1213 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1128 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 87 ; 0.145 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2794 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 345 ; 0.154 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2775 ; 1.736 ; 2.799 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2772 ; 1.640 ; 2.797 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3458 ; 2.555 ; 6.279 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3459 ; 2.556 ; 6.280 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2885 ; 2.261 ; 3.171 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2886 ; 2.261 ; 3.171 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4196 ; 3.721 ; 7.051 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4197 ; 3.720 ; 7.051 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 344 NULL REMARK 3 1 A 2 A 344 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 601 REMARK 3 ORIGIN FOR THE GROUP (A): 24.8382 38.5166 5.5503 REMARK 3 T TENSOR REMARK 3 T11: 0.0898 T22: 0.1717 REMARK 3 T33: 0.2230 T12: 0.0096 REMARK 3 T13: 0.0036 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 0.7418 L22: 0.4115 REMARK 3 L33: 0.1884 L12: 0.0476 REMARK 3 L13: -0.3197 L23: 0.0842 REMARK 3 S TENSOR REMARK 3 S11: -0.0371 S12: 0.1033 S13: -0.0411 REMARK 3 S21: 0.0597 S22: 0.0259 S23: 0.0286 REMARK 3 S31: -0.0030 S32: -0.0123 S33: 0.0112 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 26.1651 79.8326 9.0719 REMARK 3 T TENSOR REMARK 3 T11: 0.2072 T22: 0.0438 REMARK 3 T33: 0.4886 T12: 0.0848 REMARK 3 T13: 0.2401 T23: 0.0552 REMARK 3 L TENSOR REMARK 3 L11: 0.2009 L22: 1.4743 REMARK 3 L33: 0.2195 L12: 0.3543 REMARK 3 L13: -0.1973 L23: -0.4187 REMARK 3 S TENSOR REMARK 3 S11: 0.1849 S12: 0.0626 S13: 0.2882 REMARK 3 S21: 0.2654 S22: 0.1161 S23: 0.3512 REMARK 3 S31: -0.1523 S32: -0.0400 S33: -0.3010 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8OI7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129338. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68295 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 46.321 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 21.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.14900 REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.47800 REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 90 MM PIPES PH 7.0, 90 MM MGCL2, 45 MM REMARK 280 KCL, 1 MM NISO4, 14% (W/V) PEG 5000 MONOMETHYL ETHER, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.55550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 138.83325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.27775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 92.55550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.27775 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 138.83325 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 92.34400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 519 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 528 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 678 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 706 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 718 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 347 REMARK 465 MET B 1 REMARK 465 GLY B 346 REMARK 465 LYS B 347 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CB CG SD CE REMARK 470 ILE B 345 CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 682 O HOH A 723 1.98 REMARK 500 O ILE B 345 O HOH B 501 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 83 61.33 -165.26 REMARK 500 ASP A 135 -79.99 -119.96 REMARK 500 ALA A 168 144.17 -175.84 REMARK 500 PHE A 171 -58.73 -125.34 REMARK 500 ASP A 188 79.34 -151.49 REMARK 500 SER A 232 88.43 -153.77 REMARK 500 HIS A 262 -77.53 -100.62 REMARK 500 ALA A 272 72.97 -150.12 REMARK 500 ASP A 306 82.43 -155.08 REMARK 500 ASP B 135 -80.11 -117.08 REMARK 500 ALA B 168 144.15 -175.33 REMARK 500 PHE B 171 -58.83 -124.99 REMARK 500 ASP B 188 78.96 -153.09 REMARK 500 SER B 232 87.46 -152.39 REMARK 500 HIS B 262 -77.56 -101.16 REMARK 500 ASP B 306 82.46 -154.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 729 DISTANCE = 7.33 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD2 REMARK 620 2 ASP A 15 OD1 84.3 REMARK 620 3 ASP A 15 OD2 69.1 53.0 REMARK 620 4 THR A 142 O 88.3 132.8 80.8 REMARK 620 5 ASP A 263 OD2 140.2 72.0 71.1 85.2 REMARK 620 6 HOH A 536 O 70.7 133.9 137.7 85.6 147.3 REMARK 620 7 HOH A 575 O 135.8 135.8 144.5 76.3 80.3 67.1 REMARK 620 8 HOH A 628 O 105.9 70.7 123.7 154.6 96.1 79.7 79.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 22 O REMARK 620 2 VAL A 23 O 88.1 REMARK 620 3 SER A 25 O 97.0 105.8 REMARK 620 4 LEU A 28 O 98.4 164.8 87.1 REMARK 620 5 HOH A 680 O 166.2 83.7 95.9 87.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 404 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 NE2 REMARK 620 2 CYS B 79 SG 77.9 REMARK 620 3 HIS B 83 ND1 80.1 2.4 REMARK 620 4 GLU B 85 OE1 77.1 1.6 3.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 10 OD2 REMARK 620 2 ASP B 15 OD1 83.6 REMARK 620 3 ASP B 15 OD2 68.7 53.1 REMARK 620 4 THR B 142 O 88.8 132.7 80.7 REMARK 620 5 ASP B 263 OD2 140.0 73.3 71.4 83.8 REMARK 620 6 HOH B 510 O 139.5 133.3 142.5 77.0 76.6 REMARK 620 7 HOH B 543 O 69.3 133.3 135.8 85.4 148.2 71.8 REMARK 620 8 HOH B 598 O 115.9 77.7 130.3 144.8 90.9 67.9 81.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 22 O REMARK 620 2 VAL B 23 O 95.8 REMARK 620 3 SER B 25 O 95.8 112.4 REMARK 620 4 LEU B 28 O 93.4 164.2 79.3 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8OI9 RELATED DB: PDB REMARK 900 TRICHOMONAS VAGINALIS RIBOSIDE HYDROLASE IN COMPLEX WITH 5- REMARK 900 METHYLURIDINE REMARK 900 RELATED ID: 8OIA RELATED DB: PDB REMARK 900 TRICHOMONAS VAGINALIS RIBOSIDE HYDROLASE IN COMPLEX WITH D-RIBOSE REMARK 900 RELATED ID: 8OIB RELATED DB: PDB REMARK 900 TRICHOMONAS VAGINALIS RIBOSIDE HYDROLASE IN COMPLEX WITH GLYCEROL REMARK 900 RELATED ID: 8OIC RELATED DB: PDB REMARK 900 TRICHOMONAS VAGINALIS RIBOSIDE HYDROLASE (HIS-TAGGED) DBREF 8OI7 A 1 347 UNP A2FTT0 A2FTT0_TRIV3 1 347 DBREF 8OI7 B 1 347 UNP A2FTT0 A2FTT0_TRIV3 1 347 SEQRES 1 A 347 MET SER ILE LYS CYS ALA LEU ASP CYS ASP PRO GLY HIS SEQRES 2 A 347 ASP ASP LEU ALA MET ILE MET LEU ALA VAL TYR SER PRO SEQRES 3 A 347 LYS LEU ASP VAL GLN TYR ILE SER THR THR HIS GLY ASN SEQRES 4 A 347 GLN THR VAL ASN LYS THR TYR GLN ASN ALA ARG ARG THR SEQRES 5 A 347 LEU ASN LEU ILE LYS ARG ALA ASP LYS ILE PRO VAL TYR SEQRES 6 A 347 ARG GLY TYR SER LYS PRO LEU THR ARG GLU SER VAL ALA SEQRES 7 A 347 CYS PRO GLU ILE HIS GLY GLU SER GLY LEU GLY GLY VAL SEQRES 8 A 347 ASP TRP SER GLU ILE ASP ARG THR MET PRO ARG ASN PRO SEQRES 9 A 347 ALA LEU ASP ILE LEU GLY TYR LYS ASP GLU SER GLU LEU SEQRES 10 A 347 ARG PRO ASP ASP PHE PHE LYS HIS LEU HIS ARG LEU VAL SEQRES 11 A 347 SER ALA ALA GLU ASP LYS PHE ASP ILE ILE SER THR GLY SEQRES 12 A 347 SER GLU THR ASN ILE ALA GLN TYR LEU LEU ALA TYR PRO SEQRES 13 A 347 GLU ASP ALA LYS LYS ILE ARG MET THR THR MET ALA GLY SEQRES 14 A 347 ASN PHE MET ILE VAL GLY ASN ILE MET PRO PHE ALA GLU SEQRES 15 A 347 PHE ASN VAL LEU ILE ASP PRO GLU ALA ILE SER ASN ILE SEQRES 16 A 347 LEU GLN SER GLY VAL ASP TYR THR PHE ALA ALA PRO LEU SEQRES 17 A 347 ASP ILE THR HIS THR VAL LEU VAL THR GLU LYS VAL ILE SEQRES 18 A 347 ASN ASP ILE LYS ALA ALA THR GLU PRO TYR SER PRO LYS SEQRES 19 A 347 PHE THR GLU MET ILE ILE LYS LEU LEU PHE PHE PHE LYS SEQRES 20 A 347 ASP THR TYR ARG ASP VAL PHE GLY PHE ILE ASP PRO PRO SEQRES 21 A 347 LEU HIS ASP PRO VAL ALA ALA PHE HIS LEU ILE ALA PRO SEQRES 22 A 347 GLU TRP PHE GLU HIS VAL ARG CYS HIS VAL ASP ILE GLU SEQRES 23 A 347 THR LYS GLY GLU TYR THR TYR GLY CYS CYS CYS THR ASN SEQRES 24 A 347 LEU ILE LEU LYS LYS LYS ASP PRO THR LYS ILE VAL LYS SEQRES 25 A 347 PRO ASP ASN ALA THR VAL CYS LEU LYS LEU LYS GLU GLY SEQRES 26 A 347 GLY HIS ASP ALA PHE TRP ASN GLN MET ILE THR VAL TRP SEQRES 27 A 347 GLY GLU ILE ALA LYS GLU ILE GLY LYS SEQRES 1 B 347 MET SER ILE LYS CYS ALA LEU ASP CYS ASP PRO GLY HIS SEQRES 2 B 347 ASP ASP LEU ALA MET ILE MET LEU ALA VAL TYR SER PRO SEQRES 3 B 347 LYS LEU ASP VAL GLN TYR ILE SER THR THR HIS GLY ASN SEQRES 4 B 347 GLN THR VAL ASN LYS THR TYR GLN ASN ALA ARG ARG THR SEQRES 5 B 347 LEU ASN LEU ILE LYS ARG ALA ASP LYS ILE PRO VAL TYR SEQRES 6 B 347 ARG GLY TYR SER LYS PRO LEU THR ARG GLU SER VAL ALA SEQRES 7 B 347 CYS PRO GLU ILE HIS GLY GLU SER GLY LEU GLY GLY VAL SEQRES 8 B 347 ASP TRP SER GLU ILE ASP ARG THR MET PRO ARG ASN PRO SEQRES 9 B 347 ALA LEU ASP ILE LEU GLY TYR LYS ASP GLU SER GLU LEU SEQRES 10 B 347 ARG PRO ASP ASP PHE PHE LYS HIS LEU HIS ARG LEU VAL SEQRES 11 B 347 SER ALA ALA GLU ASP LYS PHE ASP ILE ILE SER THR GLY SEQRES 12 B 347 SER GLU THR ASN ILE ALA GLN TYR LEU LEU ALA TYR PRO SEQRES 13 B 347 GLU ASP ALA LYS LYS ILE ARG MET THR THR MET ALA GLY SEQRES 14 B 347 ASN PHE MET ILE VAL GLY ASN ILE MET PRO PHE ALA GLU SEQRES 15 B 347 PHE ASN VAL LEU ILE ASP PRO GLU ALA ILE SER ASN ILE SEQRES 16 B 347 LEU GLN SER GLY VAL ASP TYR THR PHE ALA ALA PRO LEU SEQRES 17 B 347 ASP ILE THR HIS THR VAL LEU VAL THR GLU LYS VAL ILE SEQRES 18 B 347 ASN ASP ILE LYS ALA ALA THR GLU PRO TYR SER PRO LYS SEQRES 19 B 347 PHE THR GLU MET ILE ILE LYS LEU LEU PHE PHE PHE LYS SEQRES 20 B 347 ASP THR TYR ARG ASP VAL PHE GLY PHE ILE ASP PRO PRO SEQRES 21 B 347 LEU HIS ASP PRO VAL ALA ALA PHE HIS LEU ILE ALA PRO SEQRES 22 B 347 GLU TRP PHE GLU HIS VAL ARG CYS HIS VAL ASP ILE GLU SEQRES 23 B 347 THR LYS GLY GLU TYR THR TYR GLY CYS CYS CYS THR ASN SEQRES 24 B 347 LEU ILE LEU LYS LYS LYS ASP PRO THR LYS ILE VAL LYS SEQRES 25 B 347 PRO ASP ASN ALA THR VAL CYS LEU LYS LEU LYS GLU GLY SEQRES 26 B 347 GLY HIS ASP ALA PHE TRP ASN GLN MET ILE THR VAL TRP SEQRES 27 B 347 GLY GLU ILE ALA LYS GLU ILE GLY LYS HET CA A 401 1 HET PEG A 402 7 HET PEG A 403 7 HET MG A 404 1 HET CA B 401 1 HET PEG B 402 7 HET MG B 403 1 HET NI B 404 1 HETNAM CA CALCIUM ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM MG MAGNESIUM ION HETNAM NI NICKEL (II) ION FORMUL 3 CA 2(CA 2+) FORMUL 4 PEG 3(C4 H10 O3) FORMUL 6 MG 2(MG 2+) FORMUL 10 NI NI 2+ FORMUL 11 HOH *358(H2 O) HELIX 1 AA1 GLY A 12 SER A 25 1 14 HELIX 2 AA2 THR A 41 ILE A 56 1 16 HELIX 3 AA3 TRP A 93 THR A 99 1 7 HELIX 4 AA4 PRO A 104 GLY A 110 1 7 HELIX 5 AA5 ASP A 113 LEU A 117 5 5 HELIX 6 AA6 ARG A 118 ASP A 121 5 4 HELIX 7 AA7 PHE A 122 ALA A 133 1 12 HELIX 8 AA8 GLU A 145 TYR A 155 1 11 HELIX 9 AA9 PRO A 156 LYS A 160 5 5 HELIX 10 AB1 GLU A 182 ILE A 187 1 6 HELIX 11 AB2 ASP A 188 SER A 198 1 11 HELIX 12 AB3 PRO A 207 HIS A 212 1 6 HELIX 13 AB4 THR A 217 GLU A 229 1 13 HELIX 14 AB5 SER A 232 PHE A 244 1 13 HELIX 15 AB6 PHE A 246 GLY A 255 1 10 HELIX 16 AB7 ASP A 263 ALA A 272 1 10 HELIX 17 AB8 PRO A 273 PHE A 276 5 4 HELIX 18 AB9 ASN A 299 ASP A 306 1 8 HELIX 19 AC1 PRO A 307 ILE A 310 5 4 HELIX 20 AC2 GLY A 325 GLY A 346 1 22 HELIX 21 AC3 GLY B 12 SER B 25 1 14 HELIX 22 AC4 THR B 41 ILE B 56 1 16 HELIX 23 AC5 PRO B 80 GLY B 84 5 5 HELIX 24 AC6 TRP B 93 THR B 99 1 7 HELIX 25 AC7 PRO B 104 GLY B 110 1 7 HELIX 26 AC8 ASP B 113 LEU B 117 5 5 HELIX 27 AC9 ARG B 118 ASP B 120 5 3 HELIX 28 AD1 ASP B 121 ALA B 133 1 13 HELIX 29 AD2 GLU B 145 TYR B 155 1 11 HELIX 30 AD3 PRO B 156 LYS B 160 5 5 HELIX 31 AD4 GLU B 182 ILE B 187 1 6 HELIX 32 AD5 ASP B 188 SER B 198 1 11 HELIX 33 AD6 PRO B 207 HIS B 212 1 6 HELIX 34 AD7 THR B 217 GLU B 229 1 13 HELIX 35 AD8 SER B 232 PHE B 244 1 13 HELIX 36 AD9 PHE B 246 GLY B 255 1 10 HELIX 37 AE1 ASP B 263 ALA B 272 1 10 HELIX 38 AE2 PRO B 273 PHE B 276 5 4 HELIX 39 AE3 ASN B 299 ASP B 306 1 8 HELIX 40 AE4 PRO B 307 ILE B 310 5 4 HELIX 41 AE5 GLY B 325 ILE B 345 1 21 SHEET 1 AA1 8 VAL A 64 ARG A 66 0 SHEET 2 AA1 8 LEU A 28 THR A 35 1 N ILE A 33 O TYR A 65 SHEET 3 AA1 8 ILE A 3 CYS A 9 1 N CYS A 5 O GLN A 31 SHEET 4 AA1 8 PHE A 137 SER A 141 1 O ILE A 140 N ASP A 8 SHEET 5 AA1 8 ILE A 162 THR A 166 1 O ARG A 163 N ILE A 139 SHEET 6 AA1 8 ASP A 201 PHE A 204 1 O ASP A 201 N MET A 164 SHEET 7 AA1 8 ALA A 316 VAL A 318 1 O THR A 317 N PHE A 204 SHEET 8 AA1 8 VAL A 279 CYS A 281 -1 N VAL A 279 O VAL A 318 SHEET 1 AA2 2 VAL A 283 ILE A 285 0 SHEET 2 AA2 2 CYS A 296 THR A 298 -1 O CYS A 297 N ASP A 284 SHEET 1 AA3 8 VAL B 64 ARG B 66 0 SHEET 2 AA3 8 LEU B 28 THR B 35 1 N ILE B 33 O TYR B 65 SHEET 3 AA3 8 ILE B 3 CYS B 9 1 N CYS B 5 O GLN B 31 SHEET 4 AA3 8 PHE B 137 SER B 141 1 O ILE B 140 N ASP B 8 SHEET 5 AA3 8 ILE B 162 THR B 166 1 O ARG B 163 N ILE B 139 SHEET 6 AA3 8 ASP B 201 PHE B 204 1 O ASP B 201 N MET B 164 SHEET 7 AA3 8 ALA B 316 VAL B 318 1 O THR B 317 N PHE B 204 SHEET 8 AA3 8 VAL B 279 CYS B 281 -1 N VAL B 279 O VAL B 318 SHEET 1 AA4 2 VAL B 283 ILE B 285 0 SHEET 2 AA4 2 CYS B 296 THR B 298 -1 O CYS B 297 N ASP B 284 LINK OD2 ASP A 10 CA CA A 401 1555 1555 2.41 LINK OD1 ASP A 15 CA CA A 401 1555 1555 2.45 LINK OD2 ASP A 15 CA CA A 401 1555 1555 2.46 LINK O ALA A 22 MG MG A 404 1555 1555 2.50 LINK O VAL A 23 MG MG A 404 1555 1555 2.39 LINK O SER A 25 MG MG A 404 1555 1555 2.28 LINK O LEU A 28 MG MG A 404 1555 1555 2.19 LINK NE2 HIS A 83 NI NI B 404 1555 3654 2.23 LINK O THR A 142 CA CA A 401 1555 1555 2.39 LINK OD2 ASP A 263 CA CA A 401 1555 1555 2.40 LINK CA CA A 401 O HOH A 536 1555 1555 2.45 LINK CA CA A 401 O HOH A 575 1555 1555 2.43 LINK CA CA A 401 O HOH A 628 1555 1555 2.42 LINK MG MG A 404 O HOH A 680 1555 1555 2.44 LINK OD2 ASP B 10 CA CA B 401 1555 1555 2.43 LINK OD1 ASP B 15 CA CA B 401 1555 1555 2.43 LINK OD2 ASP B 15 CA CA B 401 1555 1555 2.44 LINK O ALA B 22 MG MG B 403 1555 1555 2.48 LINK O VAL B 23 MG MG B 403 1555 1555 2.13 LINK O SER B 25 MG MG B 403 1555 1555 2.35 LINK O LEU B 28 MG MG B 403 1555 1555 2.48 LINK SG CYS B 79 NI NI B 404 1555 1555 2.35 LINK ND1 HIS B 83 NI NI B 404 1555 1555 1.97 LINK OE1 GLU B 85 NI NI B 404 1555 1555 1.94 LINK O THR B 142 CA CA B 401 1555 1555 2.42 LINK OD2 ASP B 263 CA CA B 401 1555 1555 2.41 LINK CA CA B 401 O HOH B 510 1555 1555 2.42 LINK CA CA B 401 O HOH B 543 1555 1555 2.43 LINK CA CA B 401 O HOH B 598 1555 1555 2.41 CISPEP 1 PRO A 11 GLY A 12 0 -15.55 CISPEP 2 PRO B 11 GLY B 12 0 -15.96 CRYST1 92.344 92.344 185.111 90.00 90.00 90.00 P 43 2 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010829 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005402 0.00000